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168  structures 109  species 1  interaction 1094  sequences 93  architectures

Family: Pentaxin (PF00354)

Summary: Pentaxin family

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Pentraxins Edit Wikipedia article

Pentaxin family
CRP pretty.png
CRP drawn from PDB 1B09
Identifiers
Symbol Pentaxin
Pfam PF00354
InterPro IPR001759
PROSITE PDOC00261
SCOP 1sac
SUPERFAMILY 1sac

Pentraxins, also known as pentaxins, are an evolutionary conserved family of proteins characterised by containing a pentraxin protein domain. Proteins of the pentraxin family are involved in acute immunological responses.[1] They are a class of pattern recognition receptors (PRRs). They are a superfamily of multifunctional conserved proteins, some of which are components of the humoral arm of innate immunity and behave as functional ancestors of antibodies (Abs). They are known as classical acute phase proteins (APP), known to the human race for over a century.[2]

Structure

Pentraxins are characterised by calcium dependent ligand binding and a distinctive flattened β-jellyroll structure similar to that of the legume lectins.[3] The name "pentraxin" is derived from the Greek word for five (penta) and berries (ragos) relating to the radial symmetry of five monomers forming a ring approximately 95Å across and 35Å deep observed in the first members of this family to be identified. The "short" pentraxins include Serum Amyloid P component (SAP) and C reactive protein (CRP). The "long" pentraxins include PTX3 (a cytokine modulated molecule) and several neuronal pentraxins.

Family members

Three of the principal members of the pentraxin family are serum proteins: namely, C-reactive protein (CRP),[4] serum amyloid P component protein (SAP),[5] and female protein (FP).[6] PTX3 (or TSG-14) protein is a cytokine-induced protein that is homologous to CRPs and SAPs, but its function has not yet been determined.

C-reactive protein

C-reactive protein is expressed during acute phase response to tissue injury or inflammation in mammals. The protein resembles antibody and performs several functions associated with host defence: it promotes agglutination, bacterial capsular swelling and phagocytosis, and activates the classical complement pathway through its calcium-dependent binding to phosphocholine.[4] CRPs have also been sequenced in an invertebrate, Limulus polyphemus (Atlantic horseshoe crab), where they are a normal constituent of the hemolymph.

Serum amyloid P component

Serum amyloid P component is a vertebrate protein that is identical to tissue forms of amyloid P component. It is found in all types of amyloid deposits, in glomerular basement menbrane and in elastic fibres in blood vessels. SAP binds to various lipoprotein ligands in a calcium-dependent manner, and it has been suggested that, in mammals, this may have important implications in atherosclerosis and amyloidosis.[5]

Hamster female protein

Hamster female protein is a SAP homologue found in Mesocricetus auratus (Golden hamster). The concentration of this plasma protein is altered by sex steroids and stimuli that elicit an acute phase response.[6]

Nervous system

Pentraxin proteins expressed in the nervous system are neural pentraxin I (NPTXI) and II (NPTXII).[7] NPTXI and NPTXII are homologous and can exist within one species. It is suggested that both proteins mediate the uptake of synaptic macromolecules and play a role in synaptic plasticity. Apexin, a sperm acrosomal protein, is a homologue of NPTXII found in Cavia porcellus (Guinea pig).[8]

Human

Human genes encoding proteins that contain this domain include:

References

  1. ^ Gewurz H, Zhang XH, Lint TF (1995). "Structure and function of the pentraxins". Curr. Opin. Immunol. 7 (1): 54–64. doi:10.1016/0952-7915(95)80029-8. PMID 7772283. 
  2. ^ Martinez de la Torre, Y; Fabbri, M (1 May 2010). "Evolution of the pentraxin family: the new entry PTX4.". Journal of immunology 184 (9): 5055 Extra |pages= or |at= (help). doi:10.4049/jimmunol.0901672. PMID 20357257. 
  3. ^ Emsley J, White HE, O'Hara BP, Oliva G, Srinivasan N, Tickle IJ, Blundell TL, Pepys MB, Wood SP (January 1994). "Structure of pentameric human serum amyloid P component". Nature 367 (6461): 338–45. doi:10.1038/367338a0. PMID 8114934. 
  4. ^ a b Romero IR, Morris C, Rodriguez M, Mold C, Du Clos TW (1998). "Inflammatory potential of C-reactive protein complexes compared to immune complexes". Clin. Immunol. Immunopathol. 87 (2): 155–162. doi:10.1006/clin.1997.4516. PMID 9614930. 
  5. ^ a b Yutani C, Shimokado K, Li XA (1998). "Serum amyloid P component associates with high density lipoprotein as well as very low density lipoprotein but not with low density lipoprotein". Biochem. Biophys. Res. Commun. 244 (1): 249–252. doi:10.1006/bbrc.1998.8248. PMID 9514915. 
  6. ^ a b Coe JE, Ross MJ (1997). "Electrophoretic polymorphism of a hamster pentraxin, female protein (amyloid P component)". Scand. J. Immunol. 46 (2): 180–182. doi:10.1046/j.1365-3083.1997.d01-109.x. PMID 9583999. 
  7. ^ Perin MS, Omeis IA, Hsu YC (1996). "Mouse and human neuronal pentraxin 1 (NPTX1): conservation, genomic structure, and chromosomal localization". Genomics 36 (3): 543–545. doi:10.1006/geno.1996.0503. PMID 8884281. 
  8. ^ Reid MS, Blobel CP (1994). "Apexin, an acrosomal pentaxin". J. Biol. Chem. 269 (51): 32615–32620. PMID 7798266. 

This article incorporates text from the public domain Pfam and InterPro IPR001759

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Pentaxin family Provide feedback

Pentaxins are also known as pentraxins.

Literature references

  1. Gewurz H, Zhang XH, Lint TF; , Curr Opin Immunol 1995;7:54-64.: Structure and function of the pentraxins. PUBMED:7772283 EPMC:7772283

  2. Srinivasan N, White HE, Emsley J, Wood SP, Pepys MB, Blundell TL; , Structure 1994;2:1017-1027.: Comparative analyses of pentraxins: implications for protomer assembly and ligand binding. PUBMED:7881902 EPMC:7881902

  3. Emsley J, White HE, O'Hara BP, Oliva G, Srinivasan N, Tickle IJ, Blundell TL, Pepys MB, Wood SP; , Nature 1994;367:338-345.: Structure of pentameric human serum amyloid P component. PUBMED:8114934 EPMC:8114934


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001759

Pentaxins (or pentraxins) [PUBMED:6356809, PUBMED:7772283] are a family of proteins which show, under electron microscopy, a discoid arrangement of five noncovalently bound subunits. Proteins of the pentaxin family are involved in acute immunological responses [PUBMED:7772283]. Three of the principal members of the pentaxin family are serum proteins: namely, C-reactive protein (CRP) [PUBMED:9614930], serum amyloid P component protein (SAP) [PUBMED:9514915], and female protein (FP) [PUBMED:9583999].

CRP is expressed during acute phase response to tissue injury or inflammation in mammals. The protein resembles antibody and performs several functions associated with host defence: it promotes agglutination, bacterial capsular swelling and phagocytosis, and activates the classical complement pathway through its calcium-dependent binding to phosphocholine. CRPs have also been sequenced in an invertebrate, Limulus polyphemus (Atlantic horseshoe crab), where they are a normal constituent of the hemolymph.

SAP is a vertebrate protein that is a precursor of amyloid component P. It is found in all types of amyloid deposits, in glomerular basement menbrane and in elastic fibres in blood vessels. SAP binds to various lipoprotein ligands in a calcium-dependent manner, and it has been suggested that, in mammals, this may have important implications in atherosclerosis and amyloidosis.

FP is a SAP homologue found in Mesocricetus auratus (Golden hamster). The concentration of this plasma protein is altered by sex steroids and stimuli that elicit an acute phase response.

Pentaxin proteins expressed in the nervous system are neural pentaxin I (NPI) and II (NPII) [PUBMED:8884281]. NPI and NPII are homologous and can exist within one species. It is suggested that both proteins mediate the uptake of synaptic macromolecules and play a role in synaptic plasticity. Apexin, a sperm acrosomal protein, is a homologue of NPII found in Cavia porcellus (Guinea pig) [PUBMED:7798266].

PTX3 (or TSG-14) protein is a cytokine-induced protein that is homologous to CRPs and SAPs, but its function is not yet known.

Domain organisation

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Pfam Clan

This family is a member of clan Concanavalin (CL0004), which has the following description:

This superfamily includes a diverse range of carbohydrate binding domains and glycosyl hydrolase enzymes that share a common structure.

The clan contains the following 16 members:

DUF1080 DUF2401 Gal-bind_lectin Glyco_hydro_11 Glyco_hydro_12 Glyco_hydro_16 Glyco_hydro_7 Laminin_G_1 Laminin_G_2 Laminin_G_3 Lectin_leg-like Lectin_legB Pentaxin Sialidase SKN1 Toxin_R_bind_N

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(9)
Full
(1094)
Representative proteomes NCBI
(1160)
Meta
(95)
RP15
(154)
RP35
(195)
RP55
(378)
RP75
(564)
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Format an alignment

  Seed
(9)
Full
(1094)
Representative proteomes NCBI
(1160)
Meta
(95)
RP15
(154)
RP35
(195)
RP55
(378)
RP75
(564)
Alignment:
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Sequence:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(9)
Full
(1094)
Representative proteomes NCBI
(1160)
Meta
(95)
RP15
(154)
RP35
(195)
RP55
(378)
RP75
(564)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Prosite
Previous IDs: pentaxin;
Type: Domain
Author: Finn RD
Number in seed: 9
Number in full: 1094
Average length of the domain: 183.20 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 30.79 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.8 20.8
Trusted cut-off 20.8 20.9
Noise cut-off 20.7 20.6
Model length: 195
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

Pentaxin

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Pentaxin domain has been found. There are 168 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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